Package javax.vecmath

Examples of javax.vecmath.Vector3f.sub()

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    q3 *= -1;
  }

  public static final Quaternion getQuaternionFrame(Point3f center, Tuple3f x, Tuple3f xy) {
    Vector3f vA = new Vector3f(x);
    vA.sub(center);
    Vector3f vB = new Vector3f(xy);
    vB.sub(center);
    return getQuaternionFrame(vA, vB, null, false);
  }
 
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  public static final Quaternion getQuaternionFrame(Point3f center, Tuple3f x, Tuple3f xy) {
    Vector3f vA = new Vector3f(x);
    vA.sub(center);
    Vector3f vB = new Vector3f(xy);
    vB.sub(center);
    return getQuaternionFrame(vA, vB, null, false);
  }
 
  public static final Quaternion getQuaternionFrame(Vector3f vA, Vector3f vB,
                                                    Vector3f vC, boolean yBased) {
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      vNH.sub(prev.getCarbonylCarbonAtom());
      */
      vNH.sub(nitrogenPoint, getLeadAtom());
      vNH.normalize();
      Vector3f v = new Vector3f();
      v.sub(nitrogenPoint, prev.getCarbonylCarbonAtom());
      v.normalize();
      vNH.add(v);
    } else {
      // Rasmol def -- just use C=O vector, so this does not account for cis-amino acids
      // but I guess if those are just proline...
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      return;
    if (widthUnitVector == null) {
      Vector3f vectorCO = new Vector3f();
      Vector3f vectorCOSum = new Vector3f();
      AminoMonomer amino = (AminoMonomer) alphaPolymer.monomers[monomerIndexFirst];
      vectorCOSum.sub(amino.getCarbonylOxygenAtom(), amino
          .getCarbonylCarbonAtom());
      for (int i = monomerCount; --i > monomerIndexFirst;) {
        amino = (AminoMonomer) alphaPolymer.monomers[i];
        vectorCO.sub(amino.getCarbonylOxygenAtom(), amino
            .getCarbonylCarbonAtom());
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        vectorCO.sub(amino.getCarbonylOxygenAtom(), amino
            .getCarbonylCarbonAtom());
        if (vectorCOSum.angle(vectorCO) < (float) Math.PI / 2)
          vectorCOSum.add(vectorCO);
        else
          vectorCOSum.sub(vectorCO);
      }
      heightUnitVector = vectorCO; // just reuse the same temp vector;
      heightUnitVector.cross(axisUnitVector, vectorCOSum);
      heightUnitVector.normalize();
      widthUnitVector = vectorCOSum;
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      pt01.set(pt00);
      pt02.set(ptTarget);
      uc.toFractional(pt01, false);
      uc.toFractional(pt02, false);
      m.transform(pt01);
      vtrans.sub(pt02, pt01);
      pt01.set(0, 0, 0);
      pt02.set(0, 0, 0);
    }
    pt01.x = pt02.y = pt03.z = 1;
    pt01.add(pt00);
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    uc.toCartesian(p1, false);
    uc.toCartesian(p2, false);
    uc.toCartesian(p3, false);

    Vector3f v01 = new Vector3f();
    v01.sub(p1, p0);
    Vector3f v02 = new Vector3f();
    v02.sub(p2, p0);
    Vector3f v03 = new Vector3f();
    v03.sub(p3, p0);
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    uc.toCartesian(p3, false);

    Vector3f v01 = new Vector3f();
    v01.sub(p1, p0);
    Vector3f v02 = new Vector3f();
    v02.sub(p2, p0);
    Vector3f v03 = new Vector3f();
    v03.sub(p3, p0);

    vtemp.cross(v01, v02);
    boolean haveinversion = (vtemp.dot(v03) < 0);
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    Vector3f v01 = new Vector3f();
    v01.sub(p1, p0);
    Vector3f v02 = new Vector3f();
    v02.sub(p2, p0);
    Vector3f v03 = new Vector3f();
    v03.sub(p3, p0);

    vtemp.cross(v01, v02);
    boolean haveinversion = (vtemp.dot(v03) < 0);

    // The first trick is to check cross products to see if we still have a
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      p3.scaleAdd(2, v03, p3);

    }

    Vector3f trans = new Vector3f(p0);
    trans.sub(pt00);
    if (trans.length() < 0.1f)
      trans = null;

    // ////////// determination of type of operation from first principles
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